Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.16.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25846	0.477
27DAP/17DAP	1.15102	0.845
39DAP/27DAP	1.01952	0.82
41DAP/39DAP	1.00282	0.92
42DAP/41DAP	1.0753	0.962
43DAP/42DAP	1.13326	1
47DAP/43DAP	1.34632	0.609
52DAP/47DAP	0.89616	0.662
57DAP/52DAP	1.12331	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92017	0.2
17DAP/reference	1.0268	0.412
27DAP/reference	1.31109	0.009
39DAP/reference	1.22843	0.026
41DAP/reference	1.08944	0.221
42DAP/reference	1.41831	0.001
43DAP/reference	1.20214	0.083
47DAP/reference	1.65962	0.001
52DAP/reference	1.41437	0.019
57DAP/reference	1.07763	0.392

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9501	0.388
27DAP/17DAP	1.05002	0.842
39DAP/27DAP	0.9098	0.283
41DAP/39DAP	1.02823	1
42DAP/41DAP	1.02606	0.984
43DAP/42DAP	1.04093	0.066
47DAP/43DAP	0.98004	0.877
52DAP/47DAP	0.85974	0.169
57DAP/52DAP	0.88079	0.334
57DAP/7DAP	0.89895	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09827	0.377
17DAP/reference	1.58248	0.006
27DAP/reference	1.46018	0.013
39DAP/reference	1.40844	0.062
41DAP/reference	1.56614	0.015
42DAP/reference	1.21677	0.1
43DAP/reference	1.51075	0.037
47DAP/reference	2.00471	0.014
52DAP/reference	1.58753	0.009
57DAP/reference	1.51237	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85052	0.296
17DAP/reference	1.36455	0.012
27DAP/reference	1.87484	0.026
39DAP/reference	1.673	0.029
41DAP/reference	2.31735	0.006
42DAP/reference	1.83969	0.007
43DAP/reference	0.99251	0.494
47DAP/reference	1.3293	0.074
52DAP/reference	1.44316	0.007
57DAP/reference	0.89912	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20138	0.224
17DAP/reference	1.18735	0.405
27DAP/reference	1.4344	0.029
39DAP/reference	1.47108	0.01
41DAP/reference	1.49328	0.03
42DAP/reference	1.75855	0.046
43DAP/reference	2.11908	0.013
47DAP/reference	2.44273	0.008
52DAP/reference	1.7737	0.04
57DAP/reference	2.68363	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92936	1
26DAP/20DAP	1.19013	0.357
34DAP/26DAP	0.99473	1
51DAP/34DAP	1.07268	0.73
52DAP/51DAP	0.905	0.151
53DAP/52DAP	0.99297	0.998
55DAP/53DAP	1.01376	1
57DAP/55DAP	1.19034	0.256
62DAP/57DAP	0.83837	0.466
68DAP/62DAP	0.98876	0.863
68DAP/14DAP	1.06094	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16516	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.46915	0.068
Mature Green Tomato/Ripe Tomato	1.39633	0.058
Immature Eggplant/Mature Eggplant	0.7823	0.111
Ripe Pepper/Ripe Tomato	0.93507	1
Mature Eggplant/Ripe Tomato	0.9314

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.05017
12-2/M82	0.71806
12-4/M82	1.11358	0.694
1-3/M82	1.07818
2-1-1/M82	1.44704
2-1/M82	N/A	N/A
2-6/M82	1.50341
3-2/M82	0.86558	1
4-1-1/M82	0.92835
4-1/M82	0.80105	1
4-3-2/M82	0.93852
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.88047	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.20366	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.72971	0.298
IL12-4/WTpooled	1.24767	0.538
IL1-4/WTpooled	0.83996
WT/WTpooled	0.99325	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.15747	0.853

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93339	1
DC3000/delta hrp 6h	0.98304	0.95
DC3000/delta hrp 12h	1.09892	1
DC3000/delta hrp 24h	1.03613	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2873	0.102
DC3000 delta B/DC3000 delta AB	1.17242	0.196

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98994	1
Exp 36h	0.86057	0.456
Exp 60h	0.84204	0.386

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.9988	1
Var 0h	1.04835	0.98
Var 12h I row2-row1	0.99494	1
Var 12h NI row2-row1	1.04103	0.649
Var 36h I row2-row1	1.26886	0.41
Var 36h NI row2-row1	0.97497	0.791
Var 60h I row2-row1	0.86045	0.285
Var 60h NI row2-row1	0.87151	0.63
Time course 0hI-0hNI	1.05166	0.662
Time course 12hI-12hNI	1.03965	0.741
Time course 36hI-36hNI	1.42524	0.005
Time course 60hI-60hNI	2.29838	0.011

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.00743	0.863
transgenic ySAMdc/azygous control (breaker)	0.7626	0.173
transgenic ySAMdc/azygous control (red)	0.8415	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02024	0.395

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40695	0.223

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15161	0.14
Manapal/WT (break)	0.94446	1
Manapal/WT (red)	1.14997	0.413